AKeco Structure Library | Resources | Beckstein Lab

The AKecoLib contains 46 models of E. coli adenylate kinase structures that were used to compare a computational approach to simulating macromolecular transitions (dynamic importance sampling) to experimentally observed structures.¹ The structures cover all conformations of AdK, from closed to open.

The structures in the library were generated by homology modelling² of the AKeco sequence on AdK structures found in the protein data bank (only variants with the LID domain were considered). For further details please refer to the paper.¹

When using these structures in your own published work please cite Beckstein et al¹.

License

Copyright © 2009 Oliver Beckstein, Elizabeth J. Denning, Thomas B. Woolf.

The structures are made available under a CreativeCommons Attributions-ShareAlike licence 3.0 ; basically you can modify and share the files but you must attribute them to us (e.g., by citing our paper) and you must make the modified files available under the same or a compatible licence.)

AKeco Library by O. Beckstein, E. J. Denning, and T. B. Woolf is licensed under a Creative Commons Attribution-ShareAlike 3.0 International License. Based on a work at http://becksteinlab.physics.asu.edu/file_download/16/AKecoLib.tar.bz2.

Data

Download the file AKecoLib.tar.bz2 und unpack the compressed archive with tar -jxvf AKecoLib.tar.bz2.

The directory AKecoLib contains files in the PDB format as written by MODELLER ². The filename (e.g. AKeco_2RH5_A.pdb) indicates (1) the PDB code of the template and (2) the chain in the template (e.g. chain A of PDB: 2RH5).

References

1. ^{a b c} O. Beckstein, E. J. Denning, J. R. Perilla, and T. B. Woolf. Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open / closed transitions. J. Mol. Biol., 394(1):160–176, 2009.
2. ^{a b} N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.